The present invention relates to hybridization.
Hybridization is a powerful and versatile technique for sequencing, detecting and localizing nucleic acids. In the general area of molecular biology, hybridization is used to map genes, detect gene expression and over-expression, diagnose diseases, identify pre-disposition to diseases, and the like. In general, labeled nucleic acid probes are hybridized to target samples and hybridization then detected. Numerous isotopic and non-isotopic systems have been developed to visualize labeled DNA probes including fluorescence-based direct detection methods, the use of digoxigeninand biotin-labeled DNA probes coupled with fluorescence detection methods or antibody-enzyme detection methods.
The target samples can be in solution or they can be immobilized on a solid surface, such as in arrays and microarrays. In microarrays, a typical method of using microarrays involves contacting nucleotide sequences contained in a fluid with the sequences immobilized on the microarrays under hybridization conditions, and then detecting the hybridization complex. The resultant pattern of hybridized nucleic acids provides information regarding the genetic profile of the sample tested. A widely used method for detecting the hybridization complex in microarrays is by fluorescence. In one method, probes derived from a biological sample are amplified in the presence of nucleotides that have been coupled to a fluorescent label (reporter) molecule so as to create labeled probes, and the labeled probes are then incubated with the microarray so that the probe sequences hybridize to the complementary sequences immobilized on the microarray. A scanner is then used to determine the levels and patterns of fluorescence.
The use of fluorescence detection in microarray analysis is disclosed in U.S. Pat. No. 5,888,742 to Lal et al. for the detection of altered expression of human phospholipid binding protein (PLBP) and in U.S. Pat. No. 5,891,674 to Hillman et al. for the monitoring of the expression level of insulin receptor tyrosine kinase substrate (IRS-p53h), and to identify its genetic variants, mutations and polymorphisms for determining gene function, and in developing and monitoring the activity of therapeutic agents.
The current hybridization methodology is generally capable of providing qualitative information only since the labels and labeling schemes used in current methodologies yield a signal that is non-quantitative. For example, in microarrays, the signal is affected by the sample to sample variation in printing, the quality and hybridization performance of each array element, and the like. One method of obtaining xe2x80x9cquantitativexe2x80x9d information, that could measure variations such as synthesis or spotting performance, hybridization performance, local noise, and the like, entails comparing the signal of interest to the signal for other genes or sequences on the microarray that act as xe2x80x9ccontrols.xe2x80x9d Such methods, however, still do not yield true quantitative information of a particular target in a sample. As such, there continues to be interest in the development of new methodologies capable of yielding quantitative information from hybridization reactions.
Methods are provided for normalizing and quantitating hybridization reactions In the subject methods, distinct polynucleotide targets and standard polynucleotide targets are contacted with detectable nucleic acid probes complementary to the distinct targets and independently detectable complements to the standard targets to produce a hybridization pattern. The hybridization pattern is then detected and used to obtain information, including quantitative information, about the amount of polynucleotides in a sample or deposited on the microarray. The independently detectable standard probes can be single stranded or double stranded. The single stranded standard probes can be sense or anti-sense, and the double stranded standard probes are sense and antisense to the standard targets. Preferably, the sense and antisense complements are present in approximately equimolar concentration. Alternatively, the double stranded probe can be a hairpin duplex wherein the sense and anti-sense strands are covalently attached.
These and other objections, advantages, and features of the invention will become apparent to those persons skilled in the art upon reading the details of the invention as more fully described below.